Fixing the Problems

The subsurface scattering material doesn't render with passes. To overcome the problem I had to separate it to five different sss materials: diffuse, front scattering, mid scattering, back scattering and specular. Then using colour buffers I was able to connect them to the custom render passes.

Here is a picture of the hypershade tree:

It worked very well. I was able to render out all of the pieces in one layer with all the passes I need.

To fix the wing specularity I simply had to add the wings to a different render layer.